Multiple sequence alignment - TraesCS1D01G017400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G017400 chr1D 100.000 3536 0 0 1 3536 7820649 7824184 0.000000e+00 6530
1 TraesCS1D01G017400 chr1D 94.227 2806 100 11 759 3536 7279403 7276632 0.000000e+00 4228
2 TraesCS1D01G017400 chr1D 84.988 2085 277 13 760 2816 7607196 7609272 0.000000e+00 2084
3 TraesCS1D01G017400 chr1D 84.424 1804 253 12 760 2537 10662410 10660609 0.000000e+00 1749
4 TraesCS1D01G017400 chr1D 93.872 767 38 6 1 759 7280774 7280009 0.000000e+00 1147
5 TraesCS1D01G017400 chr1D 77.711 1817 351 36 760 2537 494859855 494858054 0.000000e+00 1062
6 TraesCS1D01G017400 chr1D 82.234 546 85 8 219 759 7606057 7606595 8.940000e-126 460
7 TraesCS1D01G017400 chr1B 93.440 2805 117 16 759 3536 9990547 9993311 0.000000e+00 4098
8 TraesCS1D01G017400 chr1B 85.284 2093 254 28 760 2816 9557619 9555545 0.000000e+00 2109
9 TraesCS1D01G017400 chr1B 84.812 1804 244 16 760 2536 15877538 15879338 0.000000e+00 1786
10 TraesCS1D01G017400 chr1B 96.053 760 29 1 1 759 9989182 9989941 0.000000e+00 1236
11 TraesCS1D01G017400 chr1B 83.259 448 71 2 313 759 9558664 9558220 3.290000e-110 409
12 TraesCS1D01G017400 chr1B 83.377 385 64 0 375 759 15876574 15876958 1.210000e-94 357
13 TraesCS1D01G017400 chr1A 86.647 1992 239 6 760 2729 8717472 8715486 0.000000e+00 2180
14 TraesCS1D01G017400 chr1A 84.820 1805 242 16 760 2536 12504853 12506653 0.000000e+00 1786
15 TraesCS1D01G017400 chr1A 84.368 1804 254 10 760 2537 12305470 12303669 0.000000e+00 1744
16 TraesCS1D01G017400 chr1A 83.241 1802 276 10 760 2536 12209645 12207845 0.000000e+00 1631
17 TraesCS1D01G017400 chr1A 87.333 450 52 5 313 759 8718526 8718079 8.760000e-141 510
18 TraesCS1D01G017400 chr1A 85.195 385 57 0 375 759 12210636 12210252 2.560000e-106 396
19 TraesCS1D01G017400 chr1A 88.380 284 23 3 2913 3194 9252450 9252725 2.030000e-87 333
20 TraesCS1D01G017400 chr1A 98.039 102 2 0 658 759 9251945 9252046 1.010000e-40 178
21 TraesCS1D01G017400 chr2A 76.912 2092 400 41 760 2813 46825430 46823384 0.000000e+00 1110


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G017400 chr1D 7820649 7824184 3535 False 6530.0 6530 100.0000 1 3536 1 chr1D.!!$F1 3535
1 TraesCS1D01G017400 chr1D 7276632 7280774 4142 True 2687.5 4228 94.0495 1 3536 2 chr1D.!!$R3 3535
2 TraesCS1D01G017400 chr1D 10660609 10662410 1801 True 1749.0 1749 84.4240 760 2537 1 chr1D.!!$R1 1777
3 TraesCS1D01G017400 chr1D 7606057 7609272 3215 False 1272.0 2084 83.6110 219 2816 2 chr1D.!!$F2 2597
4 TraesCS1D01G017400 chr1D 494858054 494859855 1801 True 1062.0 1062 77.7110 760 2537 1 chr1D.!!$R2 1777
5 TraesCS1D01G017400 chr1B 9989182 9993311 4129 False 2667.0 4098 94.7465 1 3536 2 chr1B.!!$F1 3535
6 TraesCS1D01G017400 chr1B 9555545 9558664 3119 True 1259.0 2109 84.2715 313 2816 2 chr1B.!!$R1 2503
7 TraesCS1D01G017400 chr1B 15876574 15879338 2764 False 1071.5 1786 84.0945 375 2536 2 chr1B.!!$F2 2161
8 TraesCS1D01G017400 chr1A 12504853 12506653 1800 False 1786.0 1786 84.8200 760 2536 1 chr1A.!!$F1 1776
9 TraesCS1D01G017400 chr1A 12303669 12305470 1801 True 1744.0 1744 84.3680 760 2537 1 chr1A.!!$R1 1777
10 TraesCS1D01G017400 chr1A 8715486 8718526 3040 True 1345.0 2180 86.9900 313 2729 2 chr1A.!!$R2 2416
11 TraesCS1D01G017400 chr1A 12207845 12210636 2791 True 1013.5 1631 84.2180 375 2536 2 chr1A.!!$R3 2161
12 TraesCS1D01G017400 chr1A 9251945 9252725 780 False 255.5 333 93.2095 658 3194 2 chr1A.!!$F2 2536
13 TraesCS1D01G017400 chr2A 46823384 46825430 2046 True 1110.0 1110 76.9120 760 2813 1 chr2A.!!$R1 2053

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
24 25 1.065273 GGCATTCGCAGCATTCAGG 59.935 57.895 0.00 0.00 41.24 3.86 F
1084 1715 0.035152 CTACCATGACTTGCCAGGCA 60.035 55.000 11.22 11.22 44.64 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 2263 0.529992 GCCTTAAGCCGATGTAGCGT 60.530 55.000 0.00 0.00 34.35 5.07 R
2543 3226 1.077429 CAAAGGAGGTAGGCTGCCC 60.077 63.158 18.69 9.61 0.00 5.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.065273 GGCATTCGCAGCATTCAGG 59.935 57.895 0.00 0.00 41.24 3.86
469 479 3.948473 TGGGACAGTCGTTTTGAATGAAA 59.052 39.130 0.00 0.00 45.36 2.69
766 1391 2.614057 CGCCATGTTAAGGTGGAAGATC 59.386 50.000 9.66 0.00 37.72 2.75
883 1511 1.541310 CCTGAACCGTGAGTGCCCTA 61.541 60.000 0.00 0.00 0.00 3.53
1084 1715 0.035152 CTACCATGACTTGCCAGGCA 60.035 55.000 11.22 11.22 44.64 4.75
1617 2263 4.165180 TCCATCGGGGATTTGTTCAATCTA 59.835 41.667 0.00 0.00 42.15 1.98
1873 2519 1.141657 AGCTGCAAACTCTTGAGACCA 59.858 47.619 1.02 0.00 34.14 4.02
1990 2672 0.843984 TATGCCCCTACTTTCCAGCC 59.156 55.000 0.00 0.00 0.00 4.85
2011 2693 2.645730 ACTTCTCTCTGCGTGTGATC 57.354 50.000 0.00 0.00 0.00 2.92
2543 3226 1.737363 GCTCCGTGTCTAGCAAAGAGG 60.737 57.143 12.43 0.00 38.63 3.69
2691 3377 4.664150 TCCGACTGTATATTGTCATGCA 57.336 40.909 0.00 0.00 33.18 3.96
2692 3378 5.213891 TCCGACTGTATATTGTCATGCAT 57.786 39.130 0.00 0.00 33.18 3.96
2693 3379 5.610398 TCCGACTGTATATTGTCATGCATT 58.390 37.500 0.00 0.00 33.18 3.56
2694 3380 6.754193 TCCGACTGTATATTGTCATGCATTA 58.246 36.000 0.00 0.00 33.18 1.90
2764 3453 5.112686 GCCATCTAGAACTAAACTGAGTGG 58.887 45.833 0.00 0.00 0.00 4.00
2820 3515 4.414852 GTTTTGCTTGACGTCATATGCAT 58.585 39.130 28.76 3.79 31.15 3.96
2821 3516 5.448496 GGTTTTGCTTGACGTCATATGCATA 60.448 40.000 28.76 23.96 31.15 3.14
2822 3517 4.794248 TTGCTTGACGTCATATGCATAC 57.206 40.909 28.76 12.35 31.15 2.39
2823 3518 3.130633 TGCTTGACGTCATATGCATACC 58.869 45.455 26.37 0.00 0.00 2.73
2824 3519 2.155732 GCTTGACGTCATATGCATACCG 59.844 50.000 20.80 13.70 0.00 4.02
2825 3520 3.638484 CTTGACGTCATATGCATACCGA 58.362 45.455 20.80 14.03 0.00 4.69
2826 3521 3.282831 TGACGTCATATGCATACCGAG 57.717 47.619 15.76 12.24 0.00 4.63
2827 3522 2.621526 TGACGTCATATGCATACCGAGT 59.378 45.455 15.76 14.71 0.00 4.18
2890 3586 7.440198 TCTCTCTGTTTCCTAGATATTGCATG 58.560 38.462 0.00 0.00 0.00 4.06
2905 3601 9.745018 AGATATTGCATGGCATTACTACTTATT 57.255 29.630 0.00 0.00 38.76 1.40
3012 3708 0.236187 TGGAAATACGTGCGCAACAC 59.764 50.000 14.00 0.00 46.45 3.32
3024 3720 1.463528 GCGCAACACCTTTATCGTGTC 60.464 52.381 0.30 0.00 43.56 3.67
3028 3724 3.120649 GCAACACCTTTATCGTGTCTGAC 60.121 47.826 0.00 0.00 43.56 3.51
3068 3764 4.142924 TGTGTAGCAGTAATTTCATGTGCG 60.143 41.667 0.00 0.00 39.19 5.34
3086 3782 2.334946 GCAGCGCTGGGACATTGAA 61.335 57.895 36.47 0.00 38.20 2.69
3096 3792 3.609853 TGGGACATTGAATCTACTGCAC 58.390 45.455 0.00 0.00 0.00 4.57
3113 3809 6.636562 ACTGCACGTAGAAGTAGCTTATAT 57.363 37.500 0.00 0.00 0.00 0.86
3114 3810 6.670233 ACTGCACGTAGAAGTAGCTTATATC 58.330 40.000 0.00 0.00 0.00 1.63
3115 3811 6.262496 ACTGCACGTAGAAGTAGCTTATATCA 59.738 38.462 0.00 0.00 0.00 2.15
3116 3812 7.034685 TGCACGTAGAAGTAGCTTATATCAA 57.965 36.000 0.00 0.00 0.00 2.57
3117 3813 7.139392 TGCACGTAGAAGTAGCTTATATCAAG 58.861 38.462 0.00 0.00 0.00 3.02
3118 3814 7.012989 TGCACGTAGAAGTAGCTTATATCAAGA 59.987 37.037 0.00 0.00 0.00 3.02
3119 3815 7.535940 GCACGTAGAAGTAGCTTATATCAAGAG 59.464 40.741 0.00 0.00 0.00 2.85
3120 3816 8.561212 CACGTAGAAGTAGCTTATATCAAGAGT 58.439 37.037 0.00 0.00 0.00 3.24
3143 3839 3.250762 TCAAGACGCATTTTCCAGTTCTG 59.749 43.478 0.00 0.00 0.00 3.02
3145 3841 2.549754 AGACGCATTTTCCAGTTCTGTG 59.450 45.455 0.00 0.00 0.00 3.66
3146 3842 2.290641 GACGCATTTTCCAGTTCTGTGT 59.709 45.455 0.00 0.00 33.58 3.72
3148 3844 2.350772 CGCATTTTCCAGTTCTGTGTCC 60.351 50.000 0.00 0.00 0.00 4.02
3163 3861 7.556275 AGTTCTGTGTCCTAAGAATTTTCACAA 59.444 33.333 0.00 0.00 35.03 3.33
3221 3922 3.053619 CCCCTTGCCCTAAAGTCACTAAT 60.054 47.826 0.00 0.00 0.00 1.73
3324 4029 2.299013 GGTCCCAAAACATCCCAACTTC 59.701 50.000 0.00 0.00 0.00 3.01
3336 4041 6.784031 ACATCCCAACTTCTCAAAAGTAGAT 58.216 36.000 0.00 0.00 0.00 1.98
3341 4046 8.215050 TCCCAACTTCTCAAAAGTAGATAAACA 58.785 33.333 0.00 0.00 0.00 2.83
3342 4047 8.290325 CCCAACTTCTCAAAAGTAGATAAACAC 58.710 37.037 0.00 0.00 0.00 3.32
3365 4070 2.548920 GCCATTCTCTATCCAACTCCCG 60.549 54.545 0.00 0.00 0.00 5.14
3369 4074 3.595190 TCTCTATCCAACTCCCGATCA 57.405 47.619 0.00 0.00 0.00 2.92
3374 4079 0.976073 TCCAACTCCCGATCAGACCC 60.976 60.000 0.00 0.00 0.00 4.46
3394 4099 0.526211 CTTTTTAGCGGGGCAAGGTC 59.474 55.000 0.00 0.00 0.00 3.85
3397 4102 3.599285 TTAGCGGGGCAAGGTCGTG 62.599 63.158 0.00 0.00 0.00 4.35
3421 4126 1.817520 CGCCATCGCCAACACCATA 60.818 57.895 0.00 0.00 0.00 2.74
3436 4141 1.757118 ACCATAGTGTCGTCTCCCATG 59.243 52.381 0.00 0.00 0.00 3.66
3467 4172 1.918293 ATTGCCACCCTCTCCACGA 60.918 57.895 0.00 0.00 0.00 4.35
3485 4190 2.892425 GTCGCCTGCTTCCCATCG 60.892 66.667 0.00 0.00 0.00 3.84
3519 4224 3.005554 TGGTTTGTGTGCAAAATGTTGG 58.994 40.909 0.00 0.00 45.01 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.270839 TGCCTATTATTCTCGCCTGGC 60.271 52.381 9.11 9.11 39.53 4.85
139 141 4.886489 AGCTATTCAATTTTCTCTCAGCCC 59.114 41.667 0.00 0.00 0.00 5.19
229 237 6.581712 ACACACATTAACTTGGCAAGAAAAT 58.418 32.000 32.50 24.57 0.00 1.82
311 319 2.290367 GCTGATGCATGCGTGGTAATAA 59.710 45.455 19.18 0.00 39.41 1.40
469 479 4.166246 TCTGTACCACATCCGAGACTAT 57.834 45.455 0.00 0.00 0.00 2.12
883 1511 1.599047 CCACCGTCTTGAGCTCCAT 59.401 57.895 12.15 0.00 0.00 3.41
1617 2263 0.529992 GCCTTAAGCCGATGTAGCGT 60.530 55.000 0.00 0.00 34.35 5.07
1873 2519 1.822990 CAAGTCTTTGCTGGCATGGAT 59.177 47.619 0.00 0.00 0.00 3.41
1990 2672 3.127721 TGATCACACGCAGAGAGAAGTAG 59.872 47.826 0.00 0.00 0.00 2.57
2011 2693 6.348050 GCTTGGAAACTAAGTGTCTCATTCTG 60.348 42.308 0.00 0.00 0.00 3.02
2543 3226 1.077429 CAAAGGAGGTAGGCTGCCC 60.077 63.158 18.69 9.61 0.00 5.36
2663 3346 9.864034 CATGACAATATACAGTCGGAAATAAAC 57.136 33.333 0.00 0.00 37.58 2.01
2694 3380 9.691362 GAATTATTACAGACACAACCAACAATT 57.309 29.630 0.00 0.00 0.00 2.32
2748 3437 5.112129 ACAAACCCACTCAGTTTAGTTCT 57.888 39.130 0.00 0.00 35.71 3.01
2822 3517 9.548472 TATCATTTGATGGAGTCGGTAACTCGG 62.548 44.444 3.30 0.00 43.84 4.63
2823 3518 6.734871 TATCATTTGATGGAGTCGGTAACTCG 60.735 42.308 3.30 0.00 43.84 4.18
2824 3519 6.513180 TATCATTTGATGGAGTCGGTAACTC 58.487 40.000 3.30 0.00 43.11 3.01
2825 3520 4.819105 TCATTTGATGGAGTCGGTAACT 57.181 40.909 0.00 0.00 42.42 2.24
2826 3521 7.331193 GGTATATCATTTGATGGAGTCGGTAAC 59.669 40.741 3.30 0.00 36.05 2.50
2827 3522 7.015779 TGGTATATCATTTGATGGAGTCGGTAA 59.984 37.037 3.30 0.00 36.05 2.85
2967 3663 4.546570 GCCACTTCTGTAACATTTGAACC 58.453 43.478 0.00 0.00 0.00 3.62
3012 3708 8.622157 TCTTCTATAAGTCAGACACGATAAAGG 58.378 37.037 2.66 0.00 34.13 3.11
3068 3764 1.660560 ATTCAATGTCCCAGCGCTGC 61.661 55.000 31.96 18.66 0.00 5.25
3096 3792 9.601971 GAACTCTTGATATAAGCTACTTCTACG 57.398 37.037 0.00 0.00 0.00 3.51
3113 3809 4.024048 GGAAAATGCGTCTTGAACTCTTGA 60.024 41.667 0.00 0.00 0.00 3.02
3114 3810 4.222114 GGAAAATGCGTCTTGAACTCTTG 58.778 43.478 0.00 0.00 0.00 3.02
3115 3811 3.882888 TGGAAAATGCGTCTTGAACTCTT 59.117 39.130 0.00 0.00 0.00 2.85
3116 3812 3.476552 TGGAAAATGCGTCTTGAACTCT 58.523 40.909 0.00 0.00 0.00 3.24
3117 3813 3.251004 ACTGGAAAATGCGTCTTGAACTC 59.749 43.478 0.00 0.00 0.00 3.01
3118 3814 3.214328 ACTGGAAAATGCGTCTTGAACT 58.786 40.909 0.00 0.00 0.00 3.01
3119 3815 3.626028 ACTGGAAAATGCGTCTTGAAC 57.374 42.857 0.00 0.00 0.00 3.18
3120 3816 3.882888 AGAACTGGAAAATGCGTCTTGAA 59.117 39.130 0.00 0.00 0.00 2.69
3175 3873 4.060900 GAGGCTCTAATTCAATGCATCGA 58.939 43.478 7.40 0.00 0.00 3.59
3181 3879 3.393941 AGGGGAGAGGCTCTAATTCAATG 59.606 47.826 18.75 0.00 0.00 2.82
3233 3934 6.208840 TGGGTGTAACTCCCTAAAATTTCT 57.791 37.500 10.43 0.00 44.84 2.52
3296 4001 3.239449 GGATGTTTTGGGACCTTTCCTT 58.761 45.455 0.00 0.00 42.38 3.36
3324 4029 6.801539 TGGCTGTGTTTATCTACTTTTGAG 57.198 37.500 0.00 0.00 0.00 3.02
3336 4041 5.692115 TGGATAGAGAATGGCTGTGTTTA 57.308 39.130 0.00 0.00 0.00 2.01
3341 4046 3.135530 GGAGTTGGATAGAGAATGGCTGT 59.864 47.826 0.00 0.00 0.00 4.40
3342 4047 3.495806 GGGAGTTGGATAGAGAATGGCTG 60.496 52.174 0.00 0.00 0.00 4.85
3365 4070 2.289565 CCGCTAAAAAGGGGTCTGATC 58.710 52.381 0.55 0.00 37.16 2.92
3374 4079 0.898326 ACCTTGCCCCGCTAAAAAGG 60.898 55.000 0.00 0.00 42.57 3.11
3421 4126 0.613292 AGAGCATGGGAGACGACACT 60.613 55.000 0.00 0.00 0.00 3.55
3436 4141 3.512516 GCAATGGGCACGGAGAGC 61.513 66.667 0.00 0.00 45.24 4.09
3467 4172 2.586792 GATGGGAAGCAGGCGACT 59.413 61.111 0.00 0.00 46.44 4.18
3485 4190 6.072948 TGCACACAAACCACAACATATAGTAC 60.073 38.462 0.00 0.00 0.00 2.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.